7TCR

Methanobactin biosynthetic protein complex of MbnB and MbnC from Methylosinus trichosporium OB3b at 2.62 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis.

Park, Y.J.Jodts, R.J.Slater, J.W.Reyes, R.M.Winton, V.J.Montaser, R.A.Thomas, P.M.Dowdle, W.B.Ruiz, A.Kelleher, N.L.Bollinger Jr., J.M.Krebs, C.Hoffman, B.M.Rosenzweig, A.C.

(2022) Proc Natl Acad Sci U S A 119: e2123566119-e2123566119

  • DOI: https://doi.org/10.1073/pnas.2123566119
  • Primary Citation of Related Structures:  
    7TCR, 7TCU, 7TCW, 7TCX

  • PubMed Abstract: 

    SignificanceMethanobactins (Mbns), copper-binding peptidic compounds produced by some bacteria, are candidate therapeutics for human diseases of copper overload. The paired oxazolone-thioamide bidentate ligands of methanobactins are generated from cysteine residues in a precursor peptide, MbnA, by the MbnBC enzyme complex. MbnBC activity depends on the presence of iron and oxygen, but the catalytically active form has not been identified. Here, we provide evidence that a dinuclear Fe(II)Fe(III) center in MbnB, which is the only representative of a >13,000-member protein family to be characterized, is responsible for this reaction. These findings expand the known roles of diiron enzymes in biology and set the stage for mechanistic understanding, and ultimately engineering, of the MbnBC biosynthetic complex.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnB
A, B
268Methylosinus trichosporium OB3bMutation(s): 3 
Gene Names: mbnBCQW49_07160
UniProt
Find proteins for A0A2D2D5M1 (Methylosinus trichosporium OB3b)
Explore A0A2D2D5M1 
Go to UniProtKB:  A0A2D2D5M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2D5M1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methanobactin biosynthesis cassette protein MbnC
C, D
195Methylosinus trichosporium OB3bMutation(s): 3 
Gene Names: mbnCCQW49_07155
UniProt
Find proteins for A0A2D2CY73 (Methylosinus trichosporium OB3b)
Explore A0A2D2CY73 
Go to UniProtKB:  A0A2D2CY73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D2CY73
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.78α = 90
b = 215.64β = 90
c = 214.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118035

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection